QM/MM study of the interaction between zigzag SnC nanotube and small toxic gas molecules

Adsorptions of small toxic molecules such as CO, N₂, HCN, SO₂, H₂CO, and NH₃ on a single‐walled (6,0) SnC nanotube (SnCNT) are investigated using Quantum Mechanics/Molecular Mechanics (QM/MM) methodology. The calculations are carried out at the B3LYP/6‐311++G(d,p)//LANL2DZ:UFF level of theory. The high layer of the model consists of a pyrene‐type ring on the nanotube surface as the adsorption site, where one gas molecule is allowed to interact. Conversely, for the adsorption of the two molecules, a larger site like a coronene ring is used for the high layer. Adsorption energy, Gibbs free energy change, Mulliken charge transfer, and total electron‐density maps are computed in each case. The adsorption strength of the gas molecule on the SnCNT surface is also analyzed from the density of states projected to different atoms (PDOS) of the nanotube–adsorbate complexes. The adsorptions of CO and N₂ on the (6,0) SnCNT surface require to cross potential barriers, and the corresponding transition structures are identified by ONIOM‐IRC calculations. For the remaining four molecules, the processes of adsorption are predicted to be barrier‐less. The calculations for the adsorption of H₂CO on (5,0) and (7,0) SnCNT surfaces are extended to study the effect of the size of the nanotube. Results for the adsorption of a single molecule on (6,0) SnCNT using B3LYP functional are compared with those obtained from a dispersion corrected functional such as M06‐2X. © 2015 Wiley Periodicals, Inc.     

Theoretical study of the CO catalytic oxidation on Au/SAPO‐11 zeolite

Quantum chemistry calculations were carried out, using ONIOM2 methodology, to investigate the CO adsorption and oxidation on gold supported on Silicoaluminophospates (SAPO) molecular sieves Au/SAPO‐11 catalysts. Two models were studied, one containing one Au atom per site (Au? SAPO‐11), and the other with two Au atoms per site (Au₂? SAPO‐11). The results reveal that the CO adsorption and oxidation are exothermic on Au/SAPO11 with an ΔE of ?41.0 kcal/mol and ΔE = ?52.0 kcal/mol, for the adsorption and oxidation, respectively. On the Au₂? SAPO‐11 model, the CO adsorption and oxidation reaction occur, with a ΔE of ?29.7 kcal/mol and ?52 kcal/mol, respectively. According to our results, the oxidation reaction exhibits an Eley‐Rideal type mechanism with adsorbed CO. The theoretical calculations reveal that this type of material could be interesting to disperse Au and consequently to strengthen its catalytic use for different reactions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2573–2582, 2010     

Assessment of ab initio MP2 and density functionals for characterizing the potential energy profiles of the SN2 reactions at N center

The potential energy profiles of five selected bimolecular nucleophilic substitution (S_N2) reactions at nitrogen (N) center have been reinvestigated with the CCSD(T), G3[MP2,CCSD(T)], MP2, and some density functional methods. The basis sets of 6‐31+G(d,p) and 6‐311+G(3d,2p) are used for the MP2 and density functional calculations. Taking the relative energies at the CCSD(T)/CBS level of theory as benchmarks, we recommend the MP2, B97‐K, B2K‐PLYP, BMK, ωB97X‐D, M06‐2X, M05‐2X, CAM‐B3LYP, M08‐SO, and ωB97X methods to generally characterize the potential energy profiles for the S_N2 reactions at N center. Furthermore, these recommended methods with the relatively small 6‐31+G(d,p) basis set may also be used to perform direct classical trajectory simulations to uncover the dynamic behaviors of the S_N2 reactions at N center. © 2012 Wiley Periodicals, Inc.     

Theoretical influence of third molecule on reaction channels of weakly bound complex CO2… HF systems

In this investigation, reaction channels of weakly bound complexes CO₂…HF, CO₂…HF…NH₃, CO₂…HF…H₂O and CO₂…HF…CH₃OH systems were established at the B3LYP/6‐311++G(3df,2pd) level, using the Gaussian 98 program. The conformers of syn‐fluoroformic acid or syn‐fluoroformic acid plus a third molecule (NH₃, H₂O, or CH₃OH) were found to be more stable than the conformers of the related anti‐fluoroformic acid or anti‐fluoroformic acid plus a third molecule (NH₃, H₂O, or CH₃OH). However, the weakly bound complexes were found to be more stable than either the related syn‐ and anti‐type fluoroformic acid or the acid plus third molecule (NH₃, H₂O, or CH₃OH) conformers. They decomposed into CO₂ + HF, CO₂ + NH₄F, CO₂ + H₃OF or CO₂ + (CH₃)OH₂F combined molecular systems. The weakly bound complexes have four reaction channels, each of which includes weakly bound complexes and related systems. Moreover, each reaction channel includes two transition state structures. The transition state between the weakly bound complex and anti‐fluoroformic acid type structure (T₁₃) is significantly larger than that of internal rotation (T₂₃) between the syn‐ and anti‐FCO₂H (or FCO₂H…NH₃, FCO₂H…H₂O, or FCO₂H…CH₃OH) structures. However, adding the third molecule NH₃, H₂O, or CH₃OH can significantly reduce the activation energy of T₁₃. The catalytic strengths of the third molecules are predicted to follow the order H₂O < NH₃ < CH₃OH. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

An ONIOM and DFT study of water adsorption on rutile TiO2 (110) cluster

Density functional theory (DFT) calculations performed at ONIOM DFT B3LYP/6‐31G**‐MD/UFF level are employed to study molecular and dissociative water adsorption on rutile TiO₂ (110) surface represented by partially relaxed Ti₂₅O₃₇ ONIOM cluster. DFT calculations indicate that dissociative water adsorption is not favorable because of high activation barrier (23.2 kcal/mol). The adsorption energy and vibration frequency of both molecularly and dissociatively adsorbed water molecule on rutile TiO₂ (110) surface compare well with the values reported in the literature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Hexane Cracking over Steamed Phosphated Zeolite H‐ZSM‐5: Promotional Effect on Catalyst Performance and Stability

The nature behind the promotional effect of phosphorus on the catalytic performance and hydrothermal stability of zeolite H‐ZSM‐5 has been studied using a combination of ²⁷Al and ³¹P MAS NMR spectroscopy, soft X‐ray absorption tomography and n‐hexane catalytic cracking, complemented with NH₃ temperature‐programmed desorption and N₂ physisorption. Phosphated H‐ZSM‐5 retains more acid sites and catalytic cracking activity after steam treatment than its non‐phosphated counterpart, while the selectivity towards propylene is improved. It was established that the stabilization effect is twofold. First, the local framework silico‐aluminophosphate (SAPO) interfaces, which form after phosphatation, are not affected by steam and hold aluminum atoms fixed in the zeolite lattice, preserving the pore structure of zeolite H‐ZSM‐5. Second, the four‐coordinate framework aluminum can be forced into a reversible sixfold coordination by phosphate. These species remain stationary in the framework under hydrothermal conditions as well. Removal of physically coordinated phosphate after steam‐treatment leads to an increase in the number of strong acid sites and increased catalytic activity. We propose that the improved selectivity towards propylene during catalytic cracking can be attributed to local SAPO interfaces located at channel intersections, where they act as impediments in the formation of bulky carbenium ions and therefore suppress the bimolecular cracking mechanism.     

Characterization of acidity in [B], [Al], and [Ga] isomorphously substituted ZSM‐5: Embedded DFT/UFF approach

The structure and electronic properties of the Brønsted acid site in B, Al or Ga isomorphously substituted ZSM‐5 zeolites were studied by using quantum cluster and embedded ONIOM approaches. In the former approach, zeolites are modeled by 5T and 12T quantum clusters, where T represents a Si or Al atom. In the latter model, called “Embedded ONIOM”, the long‐range interactions of the zeolite lattice beyond the 12T quantum cluster is included via optimized point charges added to the ONIOM(B3LYP/6‐31G(d,p):UFF). Inclusion of the extended zeolitic framework covering the nanocavity has an effect on the structure and adsorption properties. We found that the OH distances and v OH of the acidic proton in zeolite obtained from both models can predict the trend of acid strength as: B‐ZSM‐5 < Ga‐ZSM‐5 < Al‐ZSM‐5, which is in very good agreement with the experimental sequence. Furthermore, the PA data calculated from E‐ONIOM is also consistent with the experimental trend: B‐ZSM‐5 < Ga‐ZSM‐5 < Al‐ZSM‐5. It has, therefore, been demonstrated that our embedded ONIOM model provides accurate performance and can be one of the useful and affordable methods for future mechanistic studies involving petrochemical reactions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

On the performance of range-separated hybrid in computations of dynamic quadratic polarizability of solution-phase organic molecules: a comparison to MP2(Full) calculation

We have assessed six range-separated hybrids (CAM-B3LYP, LC-PBE, ωB97, ωB97X, ωB97X-D and M11) in evaluating the dynamic quadratic polarizability along the direction of the molecular dipole moment, β _μ (?2ν; ν; ν; 0), by comparing with MP2(Full)-calculated data. There are 104 solution-phase organic molecules included in the set. Both geometry optimizations and β _μ (?2ν; ν; ν; 0) computations have been carried out by the same functional. Calculated results showed that simultaneous modeling geometrical and electronic effects improved significantly the nonlinear optical (NLO) property of interest. More generally, our numerical assessment revealed that the CAM-B3LYP functional could be the reasonable choice for NLO property computations.     

Effect of weak base modification on ZSM‐5 catalyst for methanol to aromatics

The effect of weak base modification on the catalytic performance of ZSM‐5 catalyst for conversion of methanol to aromatics was investigated. The catalysts were characterized using X‐ray diffraction, X‐ray fluorescence, N₂ adsorption–desorption, NH₃ temperature‐programmed desorption, Fourier transform infrared spectroscopy, scanning electron microscopy and thermogravimetry. The results showed that catalysts treated with weak base (NaHCO₃, Na₂CO₃ and NH₃⋅H₂O) exhibited a pore structure with interconnected micropores and mesopores. The existence of mesopores was beneficial for improving the diffusion of reactants and products, and the coke deposition resistance capacity of treated catalysts was enhanced greatly. Meanwhile, compared to traditional ZSM‐5 zeolite, the ratio of Brønsted to Lewis (B/L) acid sites of ZSM‐5/NH₃⋅H₂O (B/L = 7.35) zeolite slightly increased but the amount of acid sites reduced, while those of ZSM‐5/NaHCO₃ (B/L = 0.127) and ZSM‐5/Na₂CO₃ (B/L = 0.107) significantly reduced. Further, the catalyst treated with NH₃⋅H₂O solution was evaluated in the methanol to aromatics reaction and led to an enhanced aromatization reaction rate. The liquid hydrocarbons product distribution exhibited higher aromatic hydrocarbons yield (56.12%) and selectivity (40.28%) of benzene, toluene and xylene (BTX) with isoparaffin content reducing to 26.17%, which could be explained by appropriate B/L acid sites ratio, higher pore volumes and higher surface area.     

A DFT study on Cu(I) coordination in Cu‐ZSM‐5: Effects of the functional choice and tuning of the ONIOM approach

The coordination of Cu⁺ at the T1 and T7 positions of the M7 ring of Cu‐ZSM‐5, and the interaction of NO with coordinated Cu⁺ were investigated by means of DFT/ONIOM calculations. The B3LYP, BLYP, PBE1PBE, PBE, M06, and M062X functionals with the def2‐TZVP (def2‐QZVP for Cu) basis set were used in the high‐level part of ONIOM calculations, with the HF/3‐21G, B3LYP/LANL2DZ, M06/LANL2DZ, and M062X/LANL2DZ methods in the low‐level part. The ability of suitable combinations of the above methods to reproduce (i) the crystallographic structure of purely siliceous ZSM‐5, (ii) the tendency of Cu⁺ to be twofold or fourfold coordinated by framework oxygen atoms of Cu‐ZSM‐5, and (iii) the interaction energy and the N? O stretching frequency of adsorbed nitrogen oxide are discussed, showing that different results are obtained depending on the adopted computational approach. With reference to above properties, some considerations about the employment of the ONIOM approximations are also included. © 2015 Wiley Periodicals, Inc.     

Theoretical study of reaction channels for the weakly bound complex systems created with HF,CO2, and various amines

This investigation conducted reaction channels of weakly bound complexes CO₂…HF, CO₂…HF…NH₃, CO₂…HF…NH₂CH₃, CO₂…HF…NH(CH₃)₂, and CO₂…HF…N(CH₃)₃ systems, using the Gaussian 98 package at the B3LYP/6‐311++G(3df,2pd) level. The syn‐fluoroformic acid or syn‐fluoroformic acid plus NH₃ or amine conformers are more stable than the related anti‐fluoroformic acid or anti‐fluoroformic acid plus NH₃ or amine conformers. However, the above‐mentioned weakly bound complexes are more stable than both the related syn‐ and anti‐type fluoroformic acid or acid plus NH₃ or amine conformers and their related decomposed into CO₂ + HF or CO₂ + NHR₃F (R?H, CH₃) combined molecular systems. Five reaction channels of the weakly bound complexes exist. Each channel includes weakly bound complexes and their related above‐mentioned systems. Moreover, each reaction channel contains two transition states. The transition state between the weakly bound complex and anti‐fluoroformic acid type structure (T₁₃) is significantly higher than that of internal rotation (T₂₃) between syn‐ and anti‐FCO₂H (or FCO₂H…NR₃) structures. However, the above‐mentioned T₁₃ can significantly decrease its energy by adding the third molecule NH₃ or NR₃ (R?H or CH₃). The more CH₃ that is substituted in NR₃ of the reaction channel, the lower the activation energy of the transition state in the system is affected. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

The effect of surface curvature of aluminum nitride nanotubes on the adsorption of NH3

Our main objectives are to address the following fundamental issues: (1) A density functional theory study on the structural and electronic properties of the zigzag single-walled aluminum nitride nanotubes (AlNNTs) with various diameters, using B3LYP/6-31G* level of theory. (2) An ONIOM study on the curvature effect of AlNNTs on the NH₃ adsorption process using B3LYP/6-31G* and semiempirical AM1 approaches. Furthermore, a potential energy surface is calculated for NH₃ moving toward AlNNT surface. In contrast to semiconducting carbon nanotubes (Louie, Top Appl Phys 80:113, 2001) our calculations confirmed that the HOMO?CLUMO energy gap of AlNNTs increases with an increase of the tube diameter. Additionally, we showed that HOMO/LUMO interaction between NH₃ and AlNNTs becomes stronger as the tube diameter decreases.     

Relative Stability of Multiple Bonds between Germanium and Stibium. A Theoretical Study

Substituent effects on the potential energy surface of XGeSb (X=H, Li, Na, BeH, MgH, BH₂, AlH₂, CH₃, SiH₃, NH₂, PH₂, OH, SH, F, and Cl) were investigated by using B3LYP/Def2‐TZVP, B3PW91/Def2‐ TZVPP CCSD (T)//B3LYP/Def2‐TZVP methods. The isomers include structures with formal double (Ge=SbX) and triple (Xge=Sb) bonds to germanium‐stibium, so a direct comparison of these types of species is possible. Our model calculations indicate that electropositively substituted Ge=SbX species are thermodynamically and kinetically more stable than their isomeric Xge=Sb molecules. Moreover, the theoretical findings suggest that only the organic substitutions (such as CH₃) can make triply bonded Xge=Sb molecule more stable than the doubly bonded Ge=SbX species.     

The response of selected isomers of B80 buckyball toward NH3 adsorption: a density functional theory investigation

Density functional theory calculations at the B3LYP/6-31G(d) and B3LYP/6-31+G(d) levels were carried out for the adsorption of NH₃ on three symmetric isomers of B₈₀ {C ₁, T _h, I _h}. To investigate the binding features of B₈₀ isomers with NH₃, different studies including the structural and electronic parameters, the ¹⁴N electric field gradient tensors and the atoms in molecules (AIM) properties were considered. The calculated parameters by these investigations can be used as powerful tools to find out some of the unknown aspects of electronic structures of the boron buckyball and its isomers. According to previous studies, boron buckyball as an amphoteric and a hard molecule has two distinct reactive sites defined as cap and frame which act as an acid and a base, respectively. Regarding the obtained results in this study, all the isomers had the same exposure when NH₃ molecule reacted with the external wall of B₈₀. For instance, the stability of N–B bond in the cap site was significantly more than the stability of N–B bond in the frame. Moreover, the adsorption of NH₃ on frame site showed a considerable reduction in HOMO–LUMO energy gap. According to AIM theory, an electrostatic nature was observed for N–B interaction. Concerning the selected isomers of buckyball, the capability of the NH₃–B₈₀ complexes to localize electron at the N–B bond critical points depend on the reaction sites significantly. In general, ¹⁴N nuclear quadruple coupling constants and asymmetry parameter reveal a remarkable effect of NH₃ adsorption on electronic structure of the B₈₀.     

Effective removal of 2,4,6‐trinitrophenol over hexagonal metal–organic framework NH2‐MIL‐88B(Fe)

A nanostructured organic–inorganic framework, hexagonal NH₂‐MIL‐88B, has been prepared through a facile one‐pot reflux reaction and then it was characterized using various techniques. The as‐prepared sample with high specific surface area (414 m² g^?1) showed excellent adsorption for 2,4,6‐trinitrophenol (TNP) in the liquid phase. Detailed studies of the adsorption kinetics, adsorption mechanism, adsorption isotherm, activation energy and various thermodynamic parameters were conducted. The adsorption mechanism of NH₂‐MIL‐88B for TNP may be ascribed to hydrogen bond interaction, and the complexation between ─OH in TNP and unsaturated Fe(III) on the surface of NH₂‐MIL‐88B. The maximum adsorption capacity of NH₂‐MIL‐88B for TNP based on the Langmuir isotherm was 163.66 mg g^?1. The as‐prepared NH₂‐MIL‐88B adsorbent seems to be a promising material in practice for TNP removal from aqueous solution.     

Comparison of aromatic NH···π, OH···π, and CH···π interactions of alanine using MP2, CCSD, and DFT methods

A comparison of the performance of various density functional methods including long‐range corrected and dispersion corrected methods [MPW1PW91, B3LYP, B3PW91, B97‐D, B1B95, MPWB1K, M06‐2X, SVWN5, ωB97XD, long‐range correction (LC)‐ωPBE, and CAM‐B3LYP using 6‐31+G(d,p) basis set] in the study of CH···π, OH···π, and NH···π interactions were done using weak complexes of neutral (A) and cationic (A⁺) forms of alanine with benzene by taking the Møller–Plesset (MP2)/6‐31+G(d,p) results as the reference. Further, the binding energies of the neutral alanine–benzene complexes were assessed at coupled cluster (CCSD)/6‐31G(d,p) method. Analysis of the molecular geometries and interaction energies at density functional theory (DFT), MP2, CCSD methods and CCSD(T) single point level reveal that MP2 is the best overall performer for noncovalent interactions giving accuracy close to CCSD method. MPWB1K fared better in interaction energy calculations than other DFT methods. In the case of M06‐2X, SVWN5, and the dispersion corrected B97‐D, the interaction energies are significantly overrated for neutral systems compared to other methods. However, for cationic systems, B97‐D yields structures and interaction energies similar to MP2 and MPWB1K methods. Among the long‐range corrected methods, LC‐ωPBE and CAM‐B3LYP methods show close agreement with MP2 values while ωB97XD energies are notably higher than MP2 values. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

An ONIOM and DFT study of water and ammonia adsorption on anatase TiO2 (001) cluster

Density functional theory (DFT) calculations at ONIOM DFT B3LYP/ 6‐31G**‐MD/UFF level are employed to study molecular and dissociative water and ammonia adsorption on anatase TiO₂ (001) surface represented by partially relaxed Ti₂₀O₃₅ ONIOM cluster. DFT calculations indicate that water molecule is dissociated on anatase TiO₂ (001) surface by a nonactivated process with an exothermic relative energy difference of 58.12 kcal/mol. Dissociation of ammonia molecule on the same surface is energetically more favorable than molecular adsorption of ammonia (?37.17 kcal/mol vs. ?23.28 kcal/mol). The vibration frequency values also are computed for the optimized geometries of adsorbed water and ammonia molecules on anatase TiO₂ (001) surface. The computed adsorption energy and vibration frequency values are comparable with the values reported in the literature. Finally, several thermodynamical properties (ΔH°, ΔS°, and ΔG°) are calculated for temperatures corresponding to the experimental studies. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Structure and NMR spectra of cyclophanes with unsaturated bridges (cyclophenes)

The calculated structures of several known and hypothetical cyclophanes with ethylene bridges (cyclophenes) are reported together with experimental and calculated values of their NMR parameters. Of the exchange‐correlation functionals and basis sets used in this work, only the ωB97X‐D/6‐311++G(2d,2p) and ωB97X‐D/cc‐pVQZ yielded values of the C_sp3–C_sp3 bond length close to the experimental data, although significant differences still remain. As far as the NMR parameters are concerned, except for close‐lying signals, chemical shifts and coupling constants calculated at the ωB97X‐D/cc‐pVQZ level reproduce in most cases the experimental trends. Contrary to the calculations of geometries, an agreement between the values of the NMR parameters obtained at ωB97X‐D/cc‐pVQZ level and the experimental ones is the poorest compared with that of the ωB97X‐D/6‐311++G(2d,2p) one. Taking into account that the results of the different calculations show the same qualitative trends in most cases, we believe that they correctly describe the structure and properties of the hypothetical molecules studied here. Copyright © 2012 John Wiley & Sons, Ltd.